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process.log

process.log 8.9 KB
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  1. Orientation:('R', 'A', 'S')
    2. 

  2. fslmaths /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_niiData/sub-SPsT1c13m1_ses-P21_EPI.nii.gz -Tmean /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_niiData/sub-SPsT1c13m1_ses-P21_EPImean.nii.gz
    3. 

  3. bet /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_niiData/fslScaleTemp.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_niiData/sub-SPsT1c13m1_ses-P21_EPImeanBet.nii.gz -f 0.35 -m -r 45 -R -g 0.10
    4. 

  4. fslmaths /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_niiData/fslScaleTemp.nii.gz -mas /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_niiData/sub-SPsT1c13m1_ses-P21_EPImeanBet_mask.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_niiData/sub-SPsT1c13m1_ses-P21_EPIBET.nii.gz
    5. 

  5. fslsplit /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_niiData/fslScaleTemp.nii.gz sub-SPsT1c13m1_ses-P21_EPI -z
    6. 

  6. fslmerge -z /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_niiData/sub-SPsT1c13m1_ses-P21_EPI_mcf.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_mcf/sub-SPsT1c13m1_ses-P21_EPI_mcf.mat/sub-SPsT1c13m1_ses-P21_EPI0000.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_mcf/sub-SPsT1c13m1_ses-P21_EPI_mcf.mat/sub-SPsT1c13m1_ses-P21_EPI0001.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_mcf/sub-SPsT1c13m1_ses-P21_EPI_mcf.mat/sub-SPsT1c13m1_ses-P21_EPI0002.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_mcf/sub-SPsT1c13m1_ses-P21_EPI_mcf.mat/sub-SPsT1c13m1_ses-P21_EPI0003.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_mcf/sub-SPsT1c13m1_ses-P21_EPI_mcf.mat/sub-SPsT1c13m1_ses-P21_EPI0004.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_mcf/sub-SPsT1c13m1_ses-P21_EPI_mcf.mat/sub-SPsT1c13m1_ses-P21_EPI0005.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_mcf/sub-SPsT1c13m1_ses-P21_EPI_mcf.mat/sub-SPsT1c13m1_ses-P21_EPI0006.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_mcf/sub-SPsT1c13m1_ses-P21_EPI_mcf.mat/sub-SPsT1c13m1_ses-P21_EPI0007.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_mcf/sub-SPsT1c13m1_ses-P21_EPI_mcf.mat/sub-SPsT1c13m1_ses-P21_EPI0008.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_mcf/sub-SPsT1c13m1_ses-P21_EPI_mcf.mat/sub-SPsT1c13m1_ses-P21_EPI0009.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_mcf/sub-SPsT1c13m1_ses-P21_EPI_mcf.mat/sub-SPsT1c13m1_ses-P21_EPI0010.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_mcf/sub-SPsT1c13m1_ses-P21_EPI_mcf.mat/sub-SPsT1c13m1_ses-P21_EPI0011.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_mcf/sub-SPsT1c13m1_ses-P21_EPI_mcf.mat/sub-SPsT1c13m1_ses-P21_EPI0012.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_mcf/sub-SPsT1c13m1_ses-P21_EPI_mcf.mat/sub-SPsT1c13m1_ses-P21_EPI0013.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_mcf/sub-SPsT1c13m1_ses-P21_EPI_mcf.mat/sub-SPsT1c13m1_ses-P21_EPI0014.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_mcf/sub-SPsT1c13m1_ses-P21_EPI_mcf.mat/sub-SPsT1c13m1_ses-P21_EPI0015.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_mcf/sub-SPsT1c13m1_ses-P21_EPI_mcf.mat/sub-SPsT1c13m1_ses-P21_EPI0016.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_mcf/sub-SPsT1c13m1_ses-P21_EPI_mcf.mat/sub-SPsT1c13m1_ses-P21_EPI0017.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_mcf/sub-SPsT1c13m1_ses-P21_EPI_mcf.mat/sub-SPsT1c13m1_ses-P21_EPI0018.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_mcf/sub-SPsT1c13m1_ses-P21_EPI_mcf.mat/sub-SPsT1c13m1_ses-P21_EPI0019.nii.gz
    7. 

  7. fslmaths /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_niiData/sub-SPsT1c13m1_ses-P21_EPI_mcf.nii.gz -Tmean /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_niiData/sub-SPsT1c13m1_ses-P21_EPI_mcfmean.nii.gz
    8. 

  8. Error: '/data/testdata_AIDA/proc_data/Physio' has no related physio data for scan 16.I32.
    9. 

  9. Error: Processing not possible, because either there is no folder called Physio or the related physio data for the scan is missing there.
    10. 

  10. Starting Regression without slice time correction:
    11. 

  11. Regression started (wait!)
    12. 

  12. fslroi /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_niiData/sub-SPsT1c13m1_ses-P21_EPI_mcf_fslScaleTemp.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/rs-fMRI_niiData/sub-SPsT1c13m1_ses-P21_EPI_mcf_f.nii.gz 5 -1
    13. 

  13. No regression with physio data!
    14. 

  14. fslmaths /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/sub-SPsT1c13m1_ses-P21_EPI_mcf_f_RGR.nii.gz -Tmean /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/mean2.nii.gz
    15. 

  15. bet /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/mean2_fslScaleTemp.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/mean2Bet.nii.gz -f 0.35 -m -r 45 -R -g 0.10
    16. 

  16. fslmaths /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/sub-SPsT1c13m1_ses-P21_EPI_mcf_f_RGR.nii.gz -mas /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/mean2Bet_mask.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/sub-SPsT1c13m1_ses-P21_EPI_mcf_f_RGR.nii.gz
    17. 

  17. fslstats /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/sub-SPsT1c13m1_ses-P21_EPI_mcf_f_RGR.nii.gz -p 98
    18. 

  18. fslmaths /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/sub-SPsT1c13m1_ses-P21_EPI_mcf_f_RGR.nii.gz -thr 102.1429749000 -Tmin -bin /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/mask.nii.gz -odt char
    19. 

  19. fslstats /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/sub-SPsT1c13m1_ses-P21_EPI_mcf_f_RGR.nii.gz  -k /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/mask.nii.gz -p 50  
    20. 

  20. fslmaths /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/mask.nii.gz -dilF /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/mask.nii.gz
    21. 

  21. fslmaths /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/sub-SPsT1c13m1_ses-P21_EPI_mcf_f_RGR.nii.gz -mas /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/mask.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/sub-SPsT1c13m1_ses-P21_EPI_mcf_f_RGRthres.nii.gz
    22. 

  22. fslmaths /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/sub-SPsT1c13m1_ses-P21_EPI_mcf_f_RGRthres.nii.gz -Tmean /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/mean_func.nii.gz
    23. 

  23. susan /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/sub-SPsT1c13m1_ses-P21_EPI_mcf_f_RGRthres_fslScaleTemp.nii.gz 569.4900510000 1.2739827004 2 1 1 /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/mean_func_fslScaleTemp.nii.gz 569.4900510000 /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/sub-SPsT1c13m1_ses-P21_EPI_mcf_f_SRGR.nii.gz
    24. 

  24. fslmaths /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/sub-SPsT1c13m1_ses-P21_EPI_mcf_f_SRGR.nii.gz -mas /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/mask.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/sub-SPsT1c13m1_ses-P21_EPI_mcf_f_SRGR_smooth.nii.gz
    25. 

  25. fslmaths /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/sub-SPsT1c13m1_ses-P21_EPI_mcf_f_SRGR_smooth.nii.gz -mul 17.55956927 /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/sub-SPsT1c13m1_ses-P21_EPI_mcf_f_SRGR_smooth_intnorm.nii.gz
    26. 

  26. fslmaths /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/sub-SPsT1c13m1_ses-P21_EPI_mcf_f_SRGR_smooth_intnorm.nii.gz -Tmean /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/tempMean.nii.gz
    27. 

  27. fslmaths /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/sub-SPsT1c13m1_ses-P21_EPI_mcf_f_SRGR_smooth_intnorm.nii.gz -bptf 35.211268 -1.000000 -add /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/tempMean.nii.gz /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/sub-SPsT1c13m1_ses-P21_EPI_mcf_f_SFRGR.nii.gz/opt/env/lib/python3.7/site-packages/scipy/stats/stats.py:4023: PearsonRConstantInputWarning: An input array is constant; the correlation coefficient is not defined.
    28. 

  28.   warnings.warn(PearsonRConstantInputWarning())
    29. 

  29. 

  30. fslmaths /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/sub-SPsT1c13m1_ses-P21_EPI_mcf_f_SFRGR.nii.gz -thrp 17.0000000000 -Tmean -bin /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/sub-SPsT1c13m1_ses-P21_EPI_mcf_f_SFRGR_thres_mask.nii.gz -odt float
    31. 

  31. Regression completed!
    32. 

  32. sfrgr_file /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/regr/sub-SPsT1c13m1_ses-P21_EPI_mcf_f_SFRGR.nii.gz
    33. 

  33. Copy Atlas Data and generate seed ROIs
    34. 

  34. Output: /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/Seed_ROIs.nii.gz
    35. 

  35. Copy Atlas Data and generate seed ROIs
    36. 

  36. Output: /data/testdata_AIDA/proc_data/sub-SPsT1c13m1/ses-P21/func/Seed_ROIs.nii.gz
    37.